Totara 2.5.7
The kiwifruit theme renders the page header and logo in a Scorm popup window. After comparing the theme/standardtotara/layout/popup.php file to the theme/kiwifruit/layout/popup.php file, we decided to just copy the standardtotara version of this file into kiwifruit theme as a workaround. I don't think it is correct for the kiwifruit theme to attempt to render the page header in a popup.
Steps to reproduce
Create a scorm activity in a course, and set it to open in a popup
Using standardtotara or customtotara theme, open the scorm activity in the popup
Note that there is now header rendered
Now, set the site theme to kiwifruit
Open the same scorm popup activity
Notice the header being rendered in the scorm popup
Basically, kiwifruit popup.php layout file is rendering way more "stuff" than it should for a "bare" popup.